PB1700: GENOMIC CHARACTERIZATION OF CHILDHOOD B-OTHER ACUTE LEUKEMIA PATIENTS BY RNA SEQUENCING IN A SINGLE CENTER
Authors: Clara Vicente Garcés, Guerau Fernández, Elena Esperanza Cebollada, Susana Rives, Jose Luis Dapena, Mireia Camos Guijosa, Nerea Vega García
Journal: HemaSphere (2023)

Topic: 1. Acute lymphoblastic leukemia - Biology & Translational Research Background: B-cell precursor acute lymphoblastic leukemia (B-ALL) is the most frequent childhood malignancy. Genetic alterations have been used to stratify patients into recurrent leukemic subtypes impacting on diagnosis and prognosis. However, conventional methodologies fail to identify driver alterations in approximately 25-30% of B-ALL patients, and these cases are classified as B-other. A broad genomic landscape of childhood leukemia has emerged from new genomic analyses such as transcriptome sequencing (RNA-Seq). These techniques have helped to reveal new recurrent leukemogenic alterations (fusions, mutations, gene expression profiles (GEP)) with diagnostic, prognostic, and/or therapeutic value and constitute new leukemia entities. Aims: To study by RNA-Seq B-ALL patients lacking the main stratifying or recurrent gene abnormalities (B-other) to identify new biomarkers to reclassify these patients into the newly defined subtypes. Methods: The study included 44 B-other patients diagnosed at Hospital Sant Joan de Déu Barcelona from 2009 to 2022. The transcriptome of these patients was analyzed using RNA-seq in search of fusion genes and different GEPs. Fusion detection was performed using a combination of five pipelines included in the Fusion Integrative Pipeline (Fusion InPipe), and the t-SNE algorithm was used to visualize the differential GEP. Results: We included 44 pediatric B-other patients (19 female (43.2%), median age 6.7 (1.6-17.5). By RNA-seq, we were able to identify a chromosomal rearrangement in 22 cases (50%) (Table 1). We identified one patient harboring an ETV6::RUNX1 rearrangement presenting an atypical breakpoint and therefore not identified by conventional methodologies. Nineteen of the 22 patients presenting a rearrangement belonged to the recently established subtypes (ABL2, CRLF2, DUX4, ETV6, MEF2D, NUTM1, PAX5, or ZNF384 rearrangements). In addition, 4 out of these 19 patients had fusion genes not previously reported: PAX5::IGK, PAX5::PAN3, ETV6::KRT78, and IGH::SPIDR. Finally, two of the 22 patients presented fusion involving other genes (ZEB2::CXCR4 and TFG::ADGRG7) and therefore do not define the molecular category. Overall, RNA-seq allowed to reclassify half of B-other patients, based on the detection of fusion genes, providing valuable information for disease classification and prognostic stratification. Moreover, the ongoing differential expression analyses will help to refine the classification of patients in the different molecular categories based on their GEP. Table 1. Different chromosomal rearrangements identified by RNA-seq. Rearrangements colored in grey indicate not-previously reported fusion genes.Summary/Conclusion: The use of RNA-seq has allowed to refine the classification of B-other patients, allowing a more refined diagnosis or the reclassification into novel molecular subtypes of B-ALL based on the identification of fusion genes. Our results support the application of RNA-seq to achieve a more accurate risk stratification and a better follow-up of B-other leukemia patients. Keywords: ALL, RNA-seq, Chromosomal translocation, Pediatric